Abstract

Background

Recent technological advances have made it possible to efficiently genotype large
numbers of single nucleotide polymorphisms (SNPs) in livestock species, allowing the
production of high-density linkage maps. Such maps can be used for quality control
of other SNPs and for fine mapping of quantitative trait loci (QTL) via linkage disequilibrium
(LD).

Results

A high-density bovine linkage map was constructed using three types of markers. The
genotypic information was obtained from 294 microsatellites, three milk protein haplotypes
and 6769 SNPs. The map was constructed by combining genetic (linkage) and physical
information in an iterative mapping process. Markers were mapped to 3,155 unique positions;
the 6,924 autosomal markers were mapped to 3,078 unique positions and the 123 non-pseudoautosomal
and 19 pseudoautosomal sex chromosome markers were mapped to 62 and 15 unique positions,
respectively. The linkage map had a total length of 3,249 cM. For the autosomes the
average genetic distance between adjacent markers was 0.449 cM, the genetic distance
between unique map positions was 1.01 cM and the average genetic distance (cM) per
Mb was 1.25.

Conclusion

There is a high concordance between the order of the SNPs in our linkage map and their
physical positions on the most recent bovine genome sequence assembly (Btau 4.0).
The linkage maps provide support for fine mapping projects and LD studies in bovine
populations. Additionally, the linkage map may help to resolve positions of unassigned
portions of the bovine genome.